From owner-chemistry@ccl.net Mon Oct 24 04:20:00 2005 From: "Michel Petitjean ptitjean===itodys.jussieu.fr" To: CCL Subject: CCL: Re: W:Rank structure models Message-Id: <-29701-051024041531-907-Gm9TXRY9fCMIhXZ//7tUjg .. server.ccl.net> X-Original-From: Michel Petitjean Date: Mon, 24 Oct 2005 10:15:17 +0200 (MEST) Sent to CCL by: Michel Petitjean [ptitjean .. itodys.jussieu.fr] To: chemistry=-=ccl.net Subj: CCL: Re: W:Rank structure models Dear Len Salgado, Ranking docking complexes without energy calculation is difficult. A strictly geometric approach is needed. The RMS criterion is not adequate (mean of the population of the squared distances), because it acts as a superposition criterion, and of course the two proteins are not allowed to be superposed. Thus, something like a "generalized parallelism" criterion is more adequate to rank the shape complementarity. It is why I proposed to use the variance (rather than the mean) of the population of the squared distances. The major defect of this approach is that you should have knowledge of at least 7 atom-pairs participating at the protein-protein interaction. See: Solving the Geometric Docking Problem for Planar and Spatial Sets. Internet Electron. J. Mol. Des., 2002,1[4],185-192. http://www.biochempress.com M. Petitjean, > From Shape Similarity to Shape Complementarity: toward a Docking Theory. J. Math. Chem. 2004,35[3],147-158. Freeware DOG: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#DOG Michel Petitjean, Email: petitjean=-=itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean=-=ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html Sent to CCL by: "Len Salgado" [leon_salga%a%yahoo.com] > Dear * > > I've been doing protein-protein docking calculations, and let's call to the protein complexes obtained, the basic units. My final goal is to build a supramolecular structure with these basic units. The only restraint experimentally determined, defines de distance between the centre of 2 basic units. > >These supramolecular structures, could be produced by a docking procedure (and ranked accordingly), but since these structures have some thousands of residues, I've thought on obtaining them "manually", by mean of rigid rotation/translation operations on 3D space. I'm only interested on obtaining a crude view of the supramolecular protein structure, but nevertheless, want to charaterize and rank the set of supramolecular structures that I'm going to build. > >My question is. >Is there a way to rank different structure models? Is there any software/methodology which reads a set of similar structures, and ranks them by energy, for example? >Any insights will be valuable. > >Best wishes, >Len Salgado From owner-chemistry@ccl.net Mon Oct 24 04:55:00 2005 From: "C J Kenneth Tan -- OptimaNumerics cjtan,OptimaNumerics.com" To: CCL Subject: CCL: CALL FOR PAPERS - ICCSA 2006 Message-Id: <-29702-051024043431-18251-HoDEEnBG54Dl6BhfKvDBdQ*_*server.ccl.net> X-Original-From: C J Kenneth Tan -- OptimaNumerics Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Mon, 24 Oct 2005 07:08:50 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: C J Kenneth Tan -- OptimaNumerics [cjtan^_^OptimaNumerics.com] CALL FOR PAPERS - ICCSA 2006 The 2006 International Conference on Computational Science and its Applications 8-11 May 2006, The Hilton Glasgow, Scotland Computational Science has undoubtedly become a vital part of many scientific investigations, affecting researchers and practitioners in areas ranging from aerospace and automotive, to physics and chemistry, > from electronics and geosciences, to bioinformatics and internet security. Due to the sheer size of many challenges in computational science, the use of supercomputing, parallel processing, and sophisticated algorithms, is inevitable. The concentration of this Conference is in the realms of computational science in parallel and distributed environments, encompassing the facilitating theoretical foundations and the applications of such large-scale computations. You are invited to submit a paper presenting an original research in one of the following areas: 1. Computational Methods, Algorithms and Applications 2. High Performance Technical Computing and Networks 3. Advanced and Emerging Applications 4. Geometric Modelling, Graphics and Visualization 5. Information Systems and Information Technologies For the complete list of the Conference themes, and for detailed information, please visit http://www.iccsa.org WORKSHOPS / TECHNICAL SESSIONS We invite proposals for Technical Sessions/Workshops/Mini-Symposia and Tutorials in one of the conference themes. The session chairs will be responsible for all aspects of their sessions, including soliciting, reviewing, and selecting the papers. The session chairs are responsible for ensuring that only the high quality papers are accepted to their session. Proposals to organize Technical Sessions should include the following information: - title of the Technical Session - name, affiliation, mailing address and e-mail address of the proposer(s) - previous experience of the proposer in Session/Workshop organization - name, affiliation, and e-mail addresses of at least three colleagues of the proposer(s) who can comment on his (their) ability to organize a session - description of the topic of the Session (not exceeding 100 words) - a short description on how the Session will be advertised The proposal must be sent before Oct 22nd, 2005 to the e-mail address: workshops-x-iccsa.org PROCEEDINGS The proceedings of the Conference will be published in the Springer-Verlag Lecture Notes in Computer Science (LNCS) series. Based on quality and referee reviews, some papers not suitable for acceptance as Full paper will be accepted for presentation at ICCSA 2006 in Poster category and published separated from LNCS series (Book of Abstracts of Posters with ISBN number). A selected number of papers will be published as special issues in appropriate journals, such as Transactions on Computational Science, Journal of Supercomputing, International Journal of Mathematical Algorithms, and other International Journals. IMPORTANT DATES 22 October 2005: Deadline for Workshop proposal submissions 24 October 2005: Paper submission starts 21 November 2005: Deadline for paper submission (full papers) 15 January 2006: Notification of acceptance 1 February 2006: Camera Ready Papers and Pre-registration. 8 - 11 May 2006: ICCSA 2006 Conference in Glasgow, COMMITTEES Conference Chairs: Vipin Kumar (Army High Performance Computing Center and University of Minnessota, USA) Honorary Chair Marina Gavrilova (University of Calgary, Canada), Conference Co-Chair, Scientific Osvaldo Gervasi (University of Perugia) Conference Co-Chair, Program Steering Committee: Alexander V Bogdanov (Institute for High Performance Computing and Data Bases, Russia) Hyunseung Choo (Sungkyunkwan University, Korea) Marina L. Gavrilova (University of Calgary, Canada) Osvaldo Gervasi (University of Perugia, Italy) Andres Iglesias (University of Cantabria, Spain) Vipin Kumar (Army High Performance Computing Center and University of Minnessota, USA) Antonio Lagana' (University of Perugia, Italy) Heow-Pueh Lee (Institute of High Performance Computing, Singapore) Youngsong Mun (Soongsil University, Korea) C. J. Kenneth Tan (OptimaNumerics, UK), chair David Taniar (Monash University, Australia) Program Committee: Still being formed. Please visit the Conference web site for the updated list. CONTACT INFORMATION Naomi Bunn The IEE Michael Faraday House Six Hills Way Stevenage SG1 2AY United Kingdom Tel: +44 (0) 1438 765648 FAX: +44 (0) 1438 767291 e-mail: info-x-iccsa.org The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. From owner-chemistry@ccl.net Mon Oct 24 05:29:01 2005 From: "may abdelghani may01dz!=!yahoo.fr" To: CCL Subject: CCL: pi-stacking interaction with semi-empirical methods Message-Id: <-29703-051024044648-10869-6hzGHBHSjCzGbCJ5wTw4ug]~[server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 24 Oct 2005 10:46:36 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz^yahoo.fr] Hell, CCLers can semi-empirical methods( ZINDO, INDO..) treat pi-stacking interaction ( for example between a graphitic sidewall's of CNT's and bezen molecule); because, i know that there is no direct bonds between the to tow subsystems (the two subsystems keep their individuality) i hop that you can help me may abdelghani ___________________________________________________________________________ Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! Messenger Téléchargez cette version sur http://fr.messenger.yahoo.com From owner-chemistry@ccl.net Mon Oct 24 06:05:00 2005 From: "Daan van Aalten vdava:_:davapc1.bioch.dundee.ac.uk" To: CCL Subject: CCL: free software for LINUX to edit and sketch molecules Message-Id: <-29704-051024044728-10958-TSDWckBdIQD+18WJ0711Mw . server.ccl.net> X-Original-From: Daan van Aalten Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Mon, 24 Oct 2005 08:49:07 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Daan van Aalten [vdava,;,davapc1.bioch.dundee.ac.uk] Hi Vlad You can use PRODRG for this, either through the server or a local copy, see http://davapc1.bioch.dundee.ac.uk/prodrg Daan On Sun, 23 Oct 2005, Vlad Cojocaru Vlad.Cojocaru()eml-r.villa-bosch.de wrote: > > Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru*eml-r.villa-bosch.de] > Dear ccl-ers, > Can somebody indicate me a good free program for LINUX that allows me to > sketch, edit molecules and then save them as mol2 or Z-matrix files (or > at least pdb file with CONNECT records). Sybyl can do this very well but > I am wondering if there is any free software that can also do this. > Thank you > vlad > > > -- > Dr. Vlad Cojocaru > EML Research gGmbH > Molecular and Cellular Modeling Group > Villa Bosch > Schloss-Wolfsbrunnenweg 33 > 69118 Heidelberg > Germany > Phone: +49-6221-533266 > Fax: +49-6221-533298 > e-mail: Vlad.Cojocaru=-=eml-r.villa-bosch.de> > > ############################################################################## Dr. Daan van Aalten Wellcome Trust Senior Fellow / Reader Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382 344979 Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764 School of Life Sciences E-mail: see WWW page Univ. of Dundee, Dundee DD1 5EH, UK WWW: http://davapc1.bioch.dundee.ac.uk From owner-chemistry@ccl.net Mon Oct 24 06:39:00 2005 From: "Jens Thomas j.m.h.thomas- -dl.ac.uk" To: CCL Subject: CCL: free software for LINUX to edit and sketch molecules Message-Id: <-29705-051024062009-671-dlUWOntrNyhi1zOgk0PMDg() server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 24 Oct 2005 10:30:34 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas]=[dl.ac.uk] Hi Vlad The CCP1GUI ( http://www.cse.clrc.ac.uk/qcg/ccp1gui/index.shtml ) supports creating molecules as both Cartesian, Z-matrix and mixed Cartesian/Z-matrix and saving them as Z-matrices or in a variety of other output formats. Best wishes, Jens Vlad Cojocaru Vlad.Cojocaru()eml-r.villa-bosch.de wrote: >Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru*eml-r.villa-bosch.de] >Dear ccl-ers, > Can somebody indicate me a good free program for LINUX that allows me to >sketch, edit molecules and then save them as mol2 or Z-matrix files (or >at least pdb file with CONNECT records). Sybyl can do this very well but >I am wondering if there is any free software that can also do this. >Thank you >vlad > > > From owner-chemistry@ccl.net Mon Oct 24 08:47:00 2005 From: "Sebastian Rohrer sebastian.rohrer:-:mail.uni-wuerzburg.de" To: CCL Subject: CCL: OpenEye - Filter Message-Id: <-29706-051024032549-28706-3RpsV2yi+fftzOctASjPbg##server.ccl.net> X-Original-From: Sebastian Rohrer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 24 Oct 2005 08:19:46 +0200 MIME-Version: 1.0 Sent to CCL by: Sebastian Rohrer [sebastian.rohrer . mail.uni-wuerzburg.de] Hi all, in our work group we have several products from OpenEye running on both Windows and Linux machines. The license file for all programs is located on a Samba- Server to which all workstations have access and the environment variables "OE_DIR" AND "OE_LICENSE" are set accordingly, which works fine for all OpenEye products so far. When I install and try to run OpenEye's Filter, I get the message "ERROR no valid license found for Filter. Define OE_DIR environment variable". This happens on both, Linux and Windows machines. I have also tried to copy the oe_licencse.txt to the derictory where I start Filter from, with no effect. Has anybody had the same problems, and hopefully found a solution? Thanks everybody, Sebastian -- Sebastian Rohrer AK Baumann - Molecular Modelling Group Department of Pharmaceutical Chemistry Institute of Pharmacy and Food Chemistry University of Wuerzburg Am Hubland 97074 Wuerzburg Germany From owner-chemistry@ccl.net Mon Oct 24 09:22:01 2005 From: "akonuklar:_:be.itu.edu.tr" To: CCL Subject: CCL: Gaussian installation Message-Id: <-29707-051024063547-9671-soKY9vKel0mcYy0+6Wh7Hw/./server.ccl.net> X-Original-From: akonuklar*_*be.itu.edu.tr Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Sun, 23 Oct 2005 02:16:49 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: akonuklar|be.itu.edu.tr Hello After I installed the G03 to my P4 linux machine I have received an error below during the beginning of my first run. Have you ever seen such an error message? Thank you very much in advance Aylin PGFIO/stdio: No such file or directory PGFIO-F-/OPEN/unit=11/error code returned by host stdio - 2. File name = /local/gaussian_scratch/Gau-2194.inp In source file ml0.f, at line number 176 From owner-chemistry@ccl.net Mon Oct 24 09:57:00 2005 From: "Ian Hovell HOVELL/./cetem.gov.br" To: CCL Subject: CCL: CLL:Excessive number of vertices on a tessera. Message-Id: <-29708-051024084401-9122-9YT69KH90l2DUHdriLtbYQ,server.ccl.net> X-Original-From: Ian Hovell Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C5D8A0.BC750600" Date: Mon, 24 Oct 2005 10:42:11 -0300 MIME-Version: 1.0 Sent to CCL by: Ian Hovell [HOVELL]|[cetem.gov.br] This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C5D8A0.BC750600 Content-Type: text/plain; charset="iso-8859-1" Dear CCLers, On trying to model a rather large molecule in a non standard solvent (nitrobenzene) using the default gaussian model (IEF-PCM) in G03W I keep getting the following message: Excessive number of vertices on a tessera. I was wondering if anyone could throw any light on this problem and help me get around this blockage. In the mean time I will try a different solvent TIA Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Cincia e da Tecnologia- MCT Avenida Ip, No 900 - Cidade Universitaria Ilha do Fundo Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 7344 ou 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell-$-cetem.gov.br ------_=_NextPart_001_01C5D8A0.BC750600 Content-Type: text/html; charset="iso-8859-1"
 
Dear CCLers,
On trying to model a rather large molecule in a non standard solvent (nitrobenzene) using the default gaussian model (IEF-PCM) in G03W I keep getting the following message:
 
Excessive number of vertices on a tessera.
 
I was wondering if anyone could throw any light on this problem and help me get around this blockage.
 
In the mean time I will try a different solvent
 
TIA
Ian Hovell - Ph.D.
NUCLEO DE MODELAGEM MOLECULAR-NMM
Centro de Tecnologia Mineral - CETEM
Ministerio da Cincia e da Tecnologia- MCT
Avenida Ip, No 900 - Cidade Universitaria
Ilha do Fundo Rio de Janeiro RJ Brasil
CEP 21941-590
tel 00 55 (xx) 3865 7344 ou 3865 - 7216
Fax 00 55 (xx) 22602837 ou 2290-4286
e-mail hovell-$-cetem.gov.br
 
------_=_NextPart_001_01C5D8A0.BC750600-- From owner-chemistry@ccl.net Mon Oct 24 10:56:00 2005 From: "TJ O Donnell tjo__acm.org" To: CCL Subject: CCL: OpenEye - Filter Message-Id: <-29709-051024104048-18895-GhiMnYor1LuDVhza7av68Q(~)server.ccl.net> X-Original-From: "TJ O'Donnell" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 24 Oct 2005 07:40:42 -0700 MIME-Version: 1.0 Sent to CCL by: "TJ O'Donnell" [tjo-x-acm.org] Have you looked at the contents of the license file? Does it actually contain a section which allows you to use Filter? Has it expired? TJ Sebastian Rohrer sebastian.rohrer:-:mail.uni-wuerzburg.de wrote: > > Sent to CCL by: Sebastian Rohrer [sebastian.rohrer . mail.uni-wuerzburg.de] > Hi all, > > in our work group we have several products from OpenEye running on both > Windows and Linux machines. The license file for all programs is located > on a Samba- Server to which all workstations have access and the > environment variables "OE_DIR" AND "OE_LICENSE" are set accordingly, > which works fine for all OpenEye products so far. > > When I install and try to run OpenEye's Filter, I get the message "ERROR > no valid license found for Filter. Define OE_DIR environment variable". > This happens on both, Linux and Windows machines. I have also tried to > copy the oe_licencse.txt to the derictory where I start Filter from, > with no effect. > > Has anybody had the same problems, and hopefully found a solution? > > Thanks everybody, > > Sebastian > From owner-chemistry@ccl.net Mon Oct 24 11:34:00 2005 From: "Perry E. Metzger perry**piermont.com" To: CCL Subject: CCL: Ribosome computationally simulated Message-Id: <-29710-051024111804-2674-W6SfIE1t5KkPWcDwbiltTA],[server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Mon, 24 Oct 2005 11:17:54 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry*piermont.com] Some news that might make people here smile: http://www.lanl.gov/news/index.php?fuseaction=home.story&story_id=7372 LOS ALAMOS, N.M., October 19, 2005 -- Researchers at Los Alamos National Laboratory have set a new world's record by performing the first million-atom computer simulation in biology. Using the "Q Machine" supercomputer, Los Alamos computer scientists have created a molecular simulation of the cell's protein-making structure, the ribosome. The project, simulating 2.64 million atoms in motion, is more than six times larger than any biological simulations performed to date. -- Perry E. Metzger perry|piermont.com From owner-chemistry@ccl.net Mon Oct 24 12:09:00 2005 From: "Richard Wood rwoodphd+*+msn.com" To: CCL Subject: CCL: help needed Message-Id: <-29711-051024111619-2240-EmlQljclorNDOsyaeQrt3A---server.ccl.net> X-Original-From: "Richard Wood" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Mon, 24 Oct 2005 10:29:04 -0400 MIME-Version: 1.0 Sent to CCL by: "Richard Wood" [rwoodphd]|[msn.com] Hi all, I have some questions, some may be simple and some may not be. So, please bear with me :) The first is this. Where can I find a free program that runs under Windows that will read in a pdb file and do an energy minimization so that I can run dynamics calculations. The pdb files have been "generated" using psfgen that comes with NAMD. The second question may not be so simple. How can I generate "Charmm-like" topologies and parameters for small molecules? Again, I wish to use NAMD to perform dynamics calculations on these small molecules. The third one may be the most difficult. I have a protein-ligand complex that I wish to do dynamics on. The hard part is that the ligand is also a peptide. How can I set up my peptide/system so that when I generate a psf file and pdb from psfgen, it doesn't think that the peptide is part of the larger protein? Again, any programs to do this need to be free as I am doing this all freelance. Thanks in advance, Richard Richard L. Wood, Ph. D. Computational Chemist Cockeysville, MD 21030 rwoodphd#,#yahoo.com From owner-chemistry@ccl.net Mon Oct 24 14:39:01 2005 From: "Vlad Cojocaru Vlad.Cojocaru^^^eml-r.villa-bosch.de" To: CCL Subject: CCL: Gamess problem Message-Id: <-29712-051024141308-5003-4MA9Iwi0lv+cDX1YRn/ILQ]=[server.ccl.net> X-Original-From: Vlad Cojocaru Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Mon, 24 Oct 2005 20:12:47 +0200 MIME-Version: 1.0 Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru:_:eml-r.villa-bosch.de] Dear CCLers, I am encountering a strange problem when trying to use GAMESS on a single CPU (my machine). I am getting the error below. Does somebody have any idea how to fix this? "gamess.Jun202002R1.x" is the games executable. I tried both localhost or the short and long forms of my computer name but the error message was the same. I am running on a Debian Linux distribution. Thanks in advance Vlad -- Dr. Vlad Cojocaru EML Research gGmbH Molecular and Cellular Modeling Group Villa Bosch Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Germany Phone: +49-6221-533266 Fax: +49-6221-533298 e-mail: Vlad.Cojocaru~~eml-r.villa-bosch.de From owner-chemistry@ccl.net Mon Oct 24 15:33:01 2005 From: "M. L. Dodson bdodson^-^scms.utmb.edu" To: CCL Subject: CCL: help needed Message-Id: <-29713-051024150833-20821-kC3jADUAzy4UQ8MwUVg/HA : server.ccl.net> X-Original-From: "M. L. Dodson" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 24 Oct 2005 12:39:53 -0500 MIME-Version: 1.0 Sent to CCL by: "M. L. Dodson" [bdodson,scms.utmb.edu] On Monday 24 October 2005 09:29, Richard Wood rwoodphd+*+msn.com wrote: > > Sent to CCL by: "Richard Wood" [rwoodphd]|[msn.com] > Hi all, > > I have some questions, some may be simple and some may not be. So, please > bear with me :) > > The first is this. Where can I find a free program that runs under Windows > that will read in a pdb file and do an energy minimization so that I can run > dynamics calculations. The pdb files have been "generated" using psfgen > that comes with NAMD. > > The second question may not be so simple. How can I generate "Charmm-like" > topologies and parameters for small molecules? Again, I wish to use NAMD to > perform dynamics calculations on these small molecules. > > The third one may be the most difficult. I have a protein-ligand complex > that I wish to do dynamics on. The hard part is that the ligand is also a > peptide. How can I set up my peptide/system so that when I generate a psf > file and pdb from psfgen, it doesn't think that the peptide is part of the > larger protein? > > Again, any programs to do this need to be free as I am doing this all > freelance. > > Thanks in advance, > Richard > > > Richard L. Wood, Ph. D. > Computational Chemist > Cockeysville, MD 21030 > rwoodphd(~)yahoo.com > You seem to be focused on the Charmm force field. If you would consider the AMBER FF instead, then the "molecular manipulation programming language" NAB will do everything you want. But you have to write the programs to do it, typically 5-25 lines of code to do the kinds of things you describe. Starting with a PDB file of a standard protein or protein/peptide complex with only normal amino acids, a minimization program using Generalized Born methods to simulate solvation should take <10 lines, IIRC, and should just involve editing one of the furnished example programs. The language is similar to C. You can use the AMBER FF with NAMD for production dynamics. (I don't know the details, but have been told and/or read that it is straightforward.) http://www.scripps.edu/mb/case/ and click on the NAB link. Bud Dodson PS, I think inserting a "TER" record between the protein and peptide in the PDB file should do what you want. At least it would in NAB and the AMBER utilities. There is a free program, RED II, (see the AMBER web site) that can use, e.g., GAMESS or Gaussian to setup the AMBER parameters for small molecules. -- M. L. Dodson Personal: mldodson-at-houston-dot-rr-dot-com Work: bdodson-at-scms-dot-utmb-dot-edu Work: four_zero_nine-772-2178 FAX: four_zero_nine-772-1790 From owner-chemistry@ccl.net Mon Oct 24 16:08:01 2005 From: "Jim Kress ccl_nospam(-)kressworks.com" To: CCL Subject: CCL: help needed Message-Id: <-29714-051024152649-22544-nIjecOVyu92Qw9gYdighwg:-:server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 24 Oct 2005 15:26:38 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam]=[kressworks.com] Did you try Tinker? http://dasher.wustl.edu/tinker/ Jim > -----Original Message----- > From: Richard Wood rwoodphd+*+msn.com > [mailto:owner-chemistry;;ccl.net] > Sent: Monday, October 24, 2005 10:29 AM > To: Kress, Jim > Subject: CCL: help needed > > > Sent to CCL by: "Richard Wood" [rwoodphd]|[msn.com] Hi all, > > I have some questions, some may be simple and some may not > be. So, please bear with me :) > > The first is this. Where can I find a free program that runs > under Windows that will read in a pdb file and do an energy > minimization so that I can run dynamics calculations. The > pdb files have been "generated" using psfgen that comes with NAMD. > > The second question may not be so simple. How can I generate > "Charmm-like" > topologies and parameters for small molecules? Again, I wish > to use NAMD to perform dynamics calculations on these small molecules. > > The third one may be the most difficult. I have a > protein-ligand complex that I wish to do dynamics on. The > hard part is that the ligand is also a peptide. How can I > set up my peptide/system so that when I generate a psf file > and pdb from psfgen, it doesn't think that the peptide is > part of the larger protein? > > Again, any programs to do this need to be free as I am doing > this all freelance. > > Thanks in advance, > Richard > > > Richard L. Wood, Ph. D. > Computational Chemist > Cockeysville, MD 21030 > rwoodphd(~)yahoo.com > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the ;; sign. You can also look up the X-Original-From: line > in the mail header.> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > From owner-chemistry@ccl.net Mon Oct 24 16:42:01 2005 From: "Arindam Ganguly arindamganguly(a)gmail.com" To: CCL Subject: CCL: W:Calculation of Point Group Message-Id: <-29715-051024153625-25300-f7WBaqZVmoUfBgrx3V2Zkw\a/server.ccl.net> X-Original-From: Arindam Ganguly Content-Type: multipart/alternative; boundary="----=_Part_5936_3110231.1130178866193" Date: Mon, 24 Oct 2005 13:34:26 -0500 MIME-Version: 1.0 Sent to CCL by: Arindam Ganguly [arindamganguly]^[gmail.com] ------=_Part_5936_3110231.1130178866193 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Serguei, i went to the mentioned website and downloaded the symmetry.c file. i am using Bloodshed Dev C++ IDE, it can handle C files too. i build the file an= d execute but all it does is give a black command prompt box, just like we th= e one we get in WinXp. i don;t understand the mistake i am committing. further i thought probably the zip files would be the updated version but same thing happened. could you plz tell what is mistake i am making. thanks= . Arindam Ganguly On 10/21/05, Serguei Patchkovskii ps-.-ned.sims.nrc.ca< owner-chemistry^_^ccl.net> wrote: > > > Sent to CCL by: Serguei Patchkovskii [ps : ned.sims.nrc.ca > ] > > I've just tried from home (which is -definitly- not ay UofC, and it > works). In any event, if it still does not work this morning, I'll be > quite happy to e-mail you the code. > > Serguei > > On Thu, 20 Oct 2005, Dmitri Goussev dgoussev:+:wlu.ca wrot= e: > > > Serguei, I am not sure whether this page is available from non-UofC > computers. > > Dmitri > > ----- Original Message ----- > > From: Serguei Patchkovskii ps||ned.sims.nrc.ca > > To: Goussev, Dmitri > > Sent: Thursday, October 20, 2005 6:45 PM > > Subject: CCL: W:Calculation of Point Group > > > > > > > > Sent to CCL by: Serguei Patchkovskii [ps#,#ned.sims.nrc.ca] > > On Thu, 20 Oct 2005, Arindam Ganguly arindamganguly^-^gmail.com wrote: > > > > > i am looking for a software whcih when given an input of the structur= e > can > > > tell us the Point Group to which the chemical belongs too. thanks. > > > > http://www.cobalt.chem.ucalgary.ca/ps/symmetry/ > > > > The nice feature of this one is that it can also find approximate > > symmetries, and tell you how far your structure is from having the > > exact symmetry elements. > > > > Serguei > > > > --- > > Dr. Serguei Patchkovskii > > > > Tel: +1-(613)-990-0945 > > Fax: +1-(613)-947-2838 > > E-mail: Serguei.Patchkovskii * nrc.ca > > > > Coordinator of Modelling Software > > Theory and Computation Group > > Steacie Institute for Molecular Sciences > > National Research Council Canada > > Room 2011, 100 Sussex Drive > > Ottawa, Ontario > > K1A 0R6 > Canadahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/s= pammers.txt > > > > =3D------=3D_NextPart_000_0026_01C5D5C2.2F6A1420 > > Content-Type: text/html; > > charset=3D"iso-8859-1" > > Content-Transfer-Encoding: quoted-printable > > > > > > > > > charset=3D3Diso-8859-1"> > > > > > > > > > >
Serguei, I am not sure whether thi= s =3D > > page is=3D20 > > available from non-UofC computers.
> >
Dmitri 
> > > style=3D3D"PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; =3D > > BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px"> > >
----- Original Message -----
> > > style=3D3D"BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: =3D > > black">From:=3D20 > > =3D > > href=3D3D"mailto:owner-chemistry . ccl.net ">Serguei=3D= 20 > > Patchkovskii ps||ned.sims.nrc.ca > > > >
Sent: Thursday, October 20, = =3D > > 2005 6:45=3D20 > > PM
> >
Subject: CCL: W:Calculation of= =3D > > Point=3D20 > > Group
> >


Sent to CCL by: Serguei Patchkovskii=3D20 > > [ps#,#ned.sims.nrc.ca]
On Thu, 20 Oct 2005, Arindam Ganguly=3D20 > > arindamganguly^-^gmail.com wrote:

> i am looking for a =3D > > software=3D20 > > whcih when given an input of the structure can
> tell  us = =3D > > the=3D20 > > Point Group to which the chemical belongs too. thanks.

> =3D > > href=3D3D"http://www.cobalt.chem.ucalgary.ca/ps/symmetry/"> > http://www.cobal=3D > > t.chem.ucalgary.ca/ps/symmetry/ >

The=3D20 > > nice feature of this one is that it can also find approximate =3D > >
symmetries,=3D20 > > and tell you how far your structure is from having the
exact =3D > > symmetry=3D20 > > elements.

Serguei

---
Dr. Serguei =3D > > Patchkovskii

Tel:=3D20 > > +1-(613)-990-0945
Fax: +1-(613)-947-2838
E-mail: =3D > > Serguei.Patchkovskii *=3D20 > > nrc.ca

Coordinator of Modelling > Software
Theory and =3D > > Computation=3D20 > > Group
Steacie Institute for Molecular Sciences
National Research = =3D > > Council=3D20 > > Canada
Room 2011, 100 Sussex Drive
Ottawa, Ontario
K1A 0R6=3D2= 0 > > Canada



-=3D3D This is automatically added to each messag= e =3D > > by the=3D20 > > mailing script =3D3D-
To recover the email address of the author of = =3D > > the=3D20 > > message, please change
the strange characters on the top line to =3D > > the . =3D20 > > sign. You can also
look up the X-Original-From: line in the mail=3D2= 0 > > header.

E-mail to subscribers: > href=3D3D"mailto:CHEMISTRY . ccl.net ">CHEMISTRY . ccl.= net > or=3D20 > > use:
      > =3D > > href=3D3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message"> > http://www.ccl.n=3D > > et/cgi-bin/ccl/send_ccl_message

E-mail=3D20 > > to administrators: > =3D > > href=3D3D"mailto:CHEMISTRY-REQUEST . ccl.net ">CHEMISTR= Y-REQUEST > . ccl.net =3D > > or=3D20 > > use
      > =3D > > href=3D3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message"> > http://www.ccl.n=3D > > et/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:=3D20 > >
      > =3D > > href=3D3D"http://www.ccl.net/chemistry/sub_unsub.shtml"> > http://www.ccl.net/=3D > > chemistry/sub_unsub.shtml

Before=3D20 > > posting check wait time for next message at: > href=3D3D"http://www.ccl.net">http://www.ccl.net

Job =3D > > advertisements: > href=3D3D"http://www.ccl.net/jobs">http://www.ccl.net/jobs =3D > >

If your=3D20 > > mail bounces from CCL with 5.7.1 error,=3D20 > > check:
      > =3D > > href=3D3D"http://www.ccl.net/spammers.txt">http://www.ccl.net/spammers.= txt > <=3D > > > /A>

-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+= =3D > > -+-+-+-+-+



> > > > --- > Dr. Serguei Patchkovskii > > Tel: +1-(613)-990-0945 > Fax: +1-(613)-947-2838 > E-mail: Serguei.Patchkovskii:-:nrc.ca > > Coordinator of Modelling Software > Theory and Computation Group > Steacie Institute for Molecular Sciences > National Research Council Canada > Room 2011, 100 Sussex Drive > Ottawa, Ontario > K1A 0R6 Canada > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > ------=_Part_5936_3110231.1130178866193 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Serguei,
i went to the mentioned website and downloaded the symmetry.c file. i am using Bloodshed Dev C++ IDE, it can handle C files too. i build the file and execute but all it does is give a black command prompt box, just like we the one we get in WinXp. i don;t understand the mistake i am committing.
further i thought probably the zip files would be the updated version but same thing happened. could you plz tell what is mistake i am making. thanks.

Arindam Ganguly

On 10/21/05, Serguei Patchkovskii ps-.-ned.sims.nrc.ca < owner-chemistry^_^ccl.net> wrote:

Sent to CCL by: Serguei Patchkovskii [ps := =20 ned.sims.nrc.ca]

I've just tr= ied from home (which is -definitly- not ay UofC, and it
works). In any e= vent, if it still does not work this morning, I'll be
quite happy to e-m= ail you the code.

Serguei

On Thu, 20 Oct 2005, Dmitri Goussev dgoussev:+:wlu.ca wrote:

> Serguei, I am not sure w= hether this page is available from non-UofC computers.
> Dmitri
>   ----- Original Message -----
>   From: Ser= guei Patchkovskii ps||ned.sims.nrc.ca
>   To: Goussev, Dmit= ri
>   Sent: Thursday, October 20, 2005 6:45 PM
>&nbs= p;  Subject: CCL: W:Calculation of Point Group
>
>
>
>   Sent to CCL by: Serguei Patchk= ovskii [ps#,#ned.sims.nrc.ca]
>   On Thu, 20 Oct 2005, Arin= dam Ganguly arindamganguly^-^gmail.com wrote:
>
>   &= gt; i am looking for a software whcih when given an input of the structure = can
>   > tell  us the Point Group to which the c= hemical belongs too. thanks.
>
>   http://www.cobalt.chem.ucalgary.c= a/ps/symmetry/
>
>   The nice feature of this one is that it can also find appr= oximate
>   symmetries, and tell you how far your structure= is from having the
>   exact symmetry elements.
>>   Serguei
>
>   ---
>   Dr. Serguei Patchkovskii
>>   Tel: +1-(613)-990-0945
>   Fax: +1-(613)= -947-2838
>   E-mail: Serguei.Patchkovskii * nrc.ca
>
>   Coordinator of Modelling= Software
>   Theory and Computation Group
>   Steac= ie Institute for Molecular Sciences
>   National Research C= ouncil Canada
>   Room 2011, 100 Sussex Drive
> =   Ottawa, Ontario
>   K1A 0R6 Canadahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spa= mmers.txt
>
>   =3D------=3D_NextPart_000_0026_01= C5D5C2.2F6A1420
> Content-Type: text/html;
>   &= nbsp;   charset=3D"iso-8859-1"
> Content-Transfer-Encoding: quoted-printable
>
> <!D= OCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">> <HTML><HEAD>
> <META http-equiv=3D3DContent-Type= content=3D3D"text/html; =3D
> charset=3D3Diso-8859-1">
> <META content=3D3D&quo= t;MSHTML 6.00.2900.2769" name=3D3DGENERATOR>
> <STYLE>&= lt;/STYLE>
> </HEAD>
> <BODY bgColor=3D3D#ffffff>= ;
> <DIV><FONT face=3D3DArial size=3D3D2>Serguei, I am not sur= e whether this =3D
> page is=3D20
> available from non-UofC com= puters.</FONT></DIV>
> <DIV><FONT face=3D3DArial= size=3D3D2>Dmitri</FONT>&nbsp;</DIV>
> <BLOCKQUOTE=3D20
> style=3D3D"PADDING-RIGHT: 0px; PA= DDING-LEFT: 5px; MARGIN-LEFT: 5px; =3D
> BORDER-LEFT: #000000 2px sol= id; MARGIN-RIGHT: 0px">
>   <DIV style=3D3D"= ;FONT: 10pt arial">----- Original Message ----- </DIV>
>   <DIV=3D20
>   style=3D3D"BACKG= ROUND: #e4e4e4; FONT: 10pt arial; font-color: =3D
> black">&l= t;B>From:</B>=3D20
>   <A title=3D3Downer-chemi= stry . ccl.net =3D
> href=3D3D"mailto:o= wner-chemistry . ccl.net">Sergue= i=3D20
>   Patchkovskii ps||ned.sims.nrc.ca</A> </= DIV>
>   <DIV style=3D3D"FONT: 10pt arial"&= gt;<B>To:</B> <A title=3D3Ddgoussev .=20 wlu.ca=3D20
>   href=3D3D"mailto:dgoussev . wlu.ca">Goussev= , Dmitri </A> </DIV>
>   <DIV style=3D3D&quo= t;FONT: 10pt arial"><B>Sent:</B> Thursday, October 20, = =3D
> 2005 6:45=3D20
>   PM</DIV>
> &nb= sp; <DIV style=3D3D"FONT: 10pt arial"><B>Subject:<= /B> CCL: W:Calculation of =3D
> Point=3D20
>   Gro= up</DIV>
>   <DIV><BR></DIV><BR&= gt;Sent to CCL by: Serguei Patchkovskii=3D20
>   [ps#,#ned.sims.nrc.ca]<BR>On Thu, 20 Oct 2005, A= rindam Ganguly=3D20
>   arindamganguly^-^gmail.com wrote:&l= t;BR><BR>&gt; i am looking for a =3D
> software=3D20
= >   whcih when given an input of the structure can <BR>&= amp;gt; tell&nbsp; us =3D
> the=3D20
>   Point Group to which the chemical bel= ongs too. thanks.<BR><BR><A=3D20
>   =3D
= > href=3D3D"http://www.cobalt.chem.ucalgary.ca/ps/symmetry/" >http://www.cobal=3D
> t.chem.ucalgary.ca/ps/symme= try/</A><BR><BR>The=3D20
>   nice fea= ture of this one is that it can also find approximate =3D
> <BR>symmetries,=3D20
>   and tell you how fa= r your structure is from having the<BR>exact =3D
> symmetry=3D2= 0
>   elements.<BR><BR>Serguei<BR><BR&= gt;---<BR>Dr. Serguei =3D
> Patchkovskii<BR><BR>Tel:=3D20
>   +1-(= 613)-990-0945<BR>Fax: +1-(613)-947-2838<BR>E-mail: =3D
> = Serguei.Patchkovskii *=3D20
>   n= rc.ca<BR><BR>Coordinator of Modelling Software<BR>The= ory and =3D
> Computation=3D20
>   Group<BR>Steacie Instit= ute for Molecular Sciences<BR>National Research =3D
> Council= =3D20
>   Canada<BR>Room 2011, 100 Sussex Drive<BR= >Ottawa, Ontario<BR>K1A 0R6=3D20
>   Canada<BR><BR><BR><BR>-=3D3D T= his is automatically added to each message =3D
> by the=3D20
>&= nbsp;  mailing script =3D3D-<BR>To recover the email address of = the author of =3D
> the=3D20
>   message, please change<BR>the strange characters= on the top line to =3D
> the  . =3D20
>   = sign. You can also<BR>look up the X-Original-From: line in the mail= =3D20
>   header.<BR><BR>E-mail to subscribers:= <A=3D20
>   href=3D3D"mailto:CHE= MISTRY . ccl.net">CHEMISTRY . ccl.net</A> or=3D20
>   = use:<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <A=3D20
>   =3D
> href=3D3D"http://www.ccl.net/cgi-bin/ccl/send_= ccl_message">http://www.ccl.n= =3D
> et/cgi-bin/ccl/send_ccl_message</A><BR><BR&g= t;E-mail=3D20
>   to administrators: <A=3D20
>   =3D<= br>> href=3D3D"mailto:CHEMISTR= Y-REQUEST . ccl.net">CHEMISTRY-R= EQUEST . ccl.net</A> =3D
> or=3D20
>   use<BR>= &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <A=3D20
> =   =3D
> href=3D3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message&qu= ot; >http://www.ccl.n=3D
> et/= cgi-bin/ccl/send_ccl_message</A><BR><BR>Subscribe/Unsubsc= ribe:=3D20
>   <BR>&nbsp;&nbsp;&nbsp;&= ;nbsp;&nbsp; <A=3D20
>   =3D
> href=3D3D"http://www.ccl.net/chemistry/sub_unsub.= shtml">http://www.ccl.net/= =3D
> chemistry/sub_unsub.shtml</A><BR><BR>Befo= re=3D20
>   posting check wait time for next message at: <A=3D2= 0
>   href=3D3D"h= ttp://www.ccl.net">http://www.cc= l.net</A><BR><BR>Job =3D
> advertisements: <A=3D20
>   href=3D3D"http://www.ccl.net/jobs">= http://www.ccl.net/jobs</A> = =3D
> <BR><BR>If your=3D20
>   mail bounces from CCL with 5.7.1 error,=3D20
>&n= bsp;  check:<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbs= p; <A=3D20
>   =3D
> href=3D3D">http://www.ccl.net/spammers.txt<=3D
> /A><= BR><BR>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= +-+=3D
> -+-+-+-+-+<BR><BR><BR><BR></BLOCKQUOTE&= gt;</BODY></HTML>
>

---
Dr. Serguei Patchkovski= i

Tel: +1-(613)-990-0945
Fax: +1-(613)-947-2838
E-mail: Sergue= i.Patchkovskii:-:nrc.ca

Coordinator of Modelling Software
Theory and Computation GroupSteacie Institute for Molecular Sciences
National Research Council Can= ada
Room 2011, 100 Sussex Drive
Ottawa, Ontario
K1A 0R6 Canada



-=3D This is automatically added to each message by the mai= ling script =3D-
To recover the email address of the author of the messa= ge, please change
the strange characters on the top line to the ^_^ sign. = You can also
E-mail to = subscribers: CHEMISTRY^_^ccl.net or = use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_messag= e

E-mail to administrators: CHEMISTRY-REQUEST^_^ccl.net or use
    &nb= sp; http:/= /www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
      <= a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtml">http://www.ccl.net/= chemistry/sub_unsub.shtml

Before posting check wait time for nex= t message at: http://www.ccl.net

Job advertisements: http://www.ccl.net/jobs

If your mail bounces from CCL= with 5.7.1 error, check:
      

-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+= -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+



=
------=_Part_5936_3110231.1130178866193-- From owner-chemistry@ccl.net Mon Oct 24 17:18:00 2005 From: "Steve Bowlus chezbowlus]![goldrush.com" To: CCL Subject: CCL: help needed Message-Id: <-29716-051024163830-26907-emnUJGym9/gfN1qaqCvh4w::server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 24 Oct 2005 13:38:12 -0700 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus]^[goldrush.com] Hello, Richard- 1. For minimizations and dynamics I have used TINKER from the Ponder lab at Wash U in St. Louis. Windows, OSX, Linux ... he has executables for all of these. I don't know how TINKER will work with NAMD-generated pdb files - FWIW, the pdb files that TINKER generates are good input for VMD. 2. One can do small molecule work in TINKER within the limits of parameterization of the force field chosen. I use the AMBER99 parameters which I have augmented considerably to handle docked small molecules. These are not "publication grade" parameters, but I will share them if you are interested. 3. In a vanilla pdb, I would define the ligand peptide as another chain (the "B" chain if the rest of the model is a single, "A" chain). Shouldn't make any difference whether it is a "real" protein or only a fragment - the FF parameters are all the same. Alternatively, you can define all atoms in the ligand as HETATM and include the connection records. You might look at some other programs (SwissProt Viewer comes to mind) for manipulating the structure. If you use TINKER, you can start with a pdb file, but TINKER creates its own input file. Hope this helps, Steve > Sent to CCL by: "Richard Wood" [rwoodphd]|[msn.com] > Hi all, > > I have some questions, some may be simple and some may not be. So, > please bear with me :) > > The first is this. Where can I find a free program that runs under > Windows that will read in a pdb file and do an energy minimization so > that I can run dynamics calculations. The pdb files have been > "generated" using psfgen that comes with NAMD. > > The second question may not be so simple. How can I generate > "Charmm-like" topologies and parameters for small molecules? Again, I > wish to use NAMD to perform dynamics calculations on these small molecules. > > The third one may be the most difficult. I have a protein-ligand > complex that I wish to do dynamics on. The hard part is that the ligand > is also a peptide. How can I set up my peptide/system so that when I > generate a psf file and pdb from psfgen, it doesn't think that the > peptide is part of the larger protein? > > Again, any programs to do this need to be free as I am doing this all > freelance. > > Thanks in advance, > Richard > > > Richard L. Wood, Ph. D. > Computational Chemist > Cockeysville, MD 21030 > rwoodphd(~)yahoo.comhttp://www.ccl.net/chemistry/sub_unsub.shtml> > > > > From owner-chemistry@ccl.net Mon Oct 24 21:23:00 2005 From: "James J. P. Stewart mrmopac#,#worldnet.att.net" To: CCL Subject: CCL: pi-stacking interaction with semi-empirical methods Message-Id: <-29717-051024201555-22948-uP7lEtBqZDXMJ09U9u6PPA _ server.ccl.net> X-Original-From: "James J. P. Stewart" Content-Type: multipart/alternative; boundary="=====================_295025073==.ALT" Date: Mon, 24 Oct 2005 17:38:29 -0600 Mime-Version: 1.0 Sent to CCL by: "James J. P. Stewart" [mrmopac\a/worldnet.att.net] --=====================_295025073==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed None of the available semiempirical methods are good at modeling pi-stacking interactions. The fault lies in the poor modeling of the VDW attractive force. For structural modeling, I recommend molecular mechanics methods - these are much better at representing non-bonded interactions. Jimmy At 02:46 AM 10/24/2005, you wrote: >Sent to CCL by: may abdelghani [may01dz^yahoo.fr] >Hell, CCLers >can semi-empirical methods( ZINDO, INDO..) treat >pi-stacking interaction ( for example between a >graphitic sidewall's of CNT's and bezen molecule); >because, i know that there is no direct bonds between >the to tow subsystems (the two subsystems keep their >individuality) > >i hop that you can help me > >may abdelghani > ( (0) (0) ) .-----------------oOOo----(_)----oOOo--------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry LLC | E-mail: mrmopac(0)worldnet.att.net | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | | Colorado Springs CO 80921-2512 | | | USA .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo. | | .------------------------\ (----( )--------------------------------------. \_) ) / (_/ --=====================_295025073==.ALT Content-Type: text/html; charset="us-ascii" None of the available semiempirical methods are good at modeling pi-stacking interactions.

The fault lies in the poor modeling of the VDW attractive force.  For structural modeling, I recommend molecular mechanics methods - these are much better at representing non-bonded interactions.

Jimmy

At 02:46 AM 10/24/2005, you wrote:

Sent to CCL by: may abdelghani [may01dz^yahoo.fr]
Hell, CCLers
can semi-empirical methods( ZINDO, INDO..) treat
pi-stacking interaction ( for example between a
graphitic sidewall's of CNT's and bezen molecule);
because, i know that there is no direct bonds between
the to tow subsystems (the two subsystems keep their
individuality)

i hop that you can help me

may abdelghani


                         ( (0) (0) )
 .-----------------oOOo----(_)----oOOo--------------------------------------.
 | James J. P. Stewart                 |                                    |
 | Stewart Computational Chemistry LLC | E-mail:  mrmopac(0)worldnet.att.net  |
 | 15210 Paddington Circle             |  39/03/15 N, 104/49/29 W           |
 | Colorado Springs CO 80921-2512      |                                    |
 | USA                   .ooo0         | Phone: USA +(719) 488-9416         |
 |                       (   )   Oooo. |                                    |
 .------------------------\ (----(   )--------------------------------------.
                           \_)    ) /
                                 (_/ --=====================_295025073==.ALT-- From owner-chemistry@ccl.net Mon Oct 24 23:40:01 2005 From: "Dr Seth Olsen s.olsen1(_)uq.edu.au" To: CCL Subject: CCL: help needed Message-Id: <-29718-051024233428-29185-VX+Ug78Kc/0J2Pc4wJ345Q^_^server.ccl.net> X-Original-From: Dr Seth Olsen Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 25 Oct 2005 13:34:17 +1000 MIME-Version: 1.0 Sent to CCL by: Dr Seth Olsen [s.olsen1~!~uq.edu.au] Hi Richard, You may find your options are greater if you use something like Cygwin under windows. I couldn't get that technical about the description, but Cygwin essentially gives you a linux-imitating environment that runs under windows. This will allow you to set up some linux software for use, which will make the requirement that the software be free easier to deal with. There is a lot more open-source and free material available to run under linux systems. Also, anything written in python should be platform-independent, and in principle should be able to be set up under windows. Although I have never used MMTK under windows, you might give it a look to see if it can be used. If not under windows per se, than it almost certainly can be set up under cygwin. MMTK can run minimizations, but right now CHARMM is not an implemented force field. However, you may find that it's library-like structure is quite nice for coding your own tools to do things that you need (I have found this to be the case). Cygwin is free. I think the site is www.cygwin.org or somesuch. Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1*o*uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms ----- Original Message ----- > From: "Richard Wood rwoodphd+*+msn.com" Date: Tuesday, October 25, 2005 0:29 am Subject: CCL: help needed > > Sent to CCL by: "Richard Wood" [rwoodphd]|[msn.com] > Hi all, > > I have some questions, some may be simple and some may not be. So, > please > bear with me :) > > The first is this. Where can I find a free program that runs under > Windows > that will read in a pdb file and do an energy minimization so that > I can run > dynamics calculations. The pdb files have been "generated" using > psfgen > that comes with NAMD. > > The second question may not be so simple. How can I generate > "Charmm-like" > topologies and parameters for small molecules? Again, I wish to > use NAMD to > perform dynamics calculations on these small molecules. > > The third one may be the most difficult. I have a protein-ligand > complex > that I wish to do dynamics on. The hard part is that the ligand is > also a > peptide. How can I set up my peptide/system so that when I > generate a psf > file and pdb from psfgen, it doesn't think that the peptide is part > of the > larger protein? > > Again, any programs to do this need to be free as I am doing this > all > freelance. > > Thanks in advance, > Richard > > > Richard L. Wood, Ph. D. > Computational Chemist > Cockeysville, MD 21030 > rwoodphd(~)yahoo.com > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the *o* sign. You can > also> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > >